VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 08 2007 - 00:51:52 CDT

Dear VMD-L,
  I've just posted VMD 1.8.6 on the web site for download:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/

In addition to the officially-supported binaries, some unofficial RPM
versions and other user-contributed builds will likely be coming as
time allows.

For those of you that haven't seen the beta versions we've made available,
here's the list of new features and improvements found in this version:

What's new in VMD 1.8.6?
------------------------
  User documentation updates
    o Minor improvements and corrections to the VMD User's Guide,
      added documentation for new commands and environment variables.
    o New and updated tutorials available for advanced images and movie making,
      3-D PDF export, Tachyon ambient occlusion lighting,
      electrostatic surface coloring, and density map based atom selections.

  User interface changes
    o New "User" picking mode for use with user defined scripts and plugins

  General Improvements
    o New Windows InstallShield installer better supports systems running
      Windows XP x64 and Vista x64.
    o Support for 3-D capture with Acrobat 3-D, for creation of
      documents which embed 3-D molecular structures.
    o VMD renderings can now use Tachyon's advanced ambient occlusion lighting
      for tremendously improved 3-D renderings of molecular graphics.
      This advanced lighting mode can greatly enhance the shading of
      pores and channels, structures with cavities, and other cases which
      typically require the use of depth cueing for better depth perception.
    o VMD now supports the nVidia "Gelato" GPU-accelerated
      production quality rendering package. VMD exports scenes in
      Gelato's native PYG file format, as well as the RenderMan RIB format.
    o By default VMD will now use all of the available processors to
      accelerate parallelized portions of the code which currently include
      several structure analysis routines, Interactive MD, and ray tracing.
    o Overall per-atom memory use has been significantly decreased.
      VMD now uses just over half as much memory per atom compared with
      previous versions, leaving more space available for additional
      trajectory frames or for more molecules to be loaded at once.
    o VMD structure loading and analysis scalability have been
      significantly improved. VMD has been successfully tested
      loading and analyzing structures of up to 72,000,000 atoms.
    o Automatic bond determination algorithm now runs up to 3 times
      faster on single processor systems, and uses multiple processors
      for improved performance on multicore processors and multiprocessor
      workstations.
    o Drastically improved multi-thousand-file structure loading
      performance when display update is disabled. This benefits
      batch mode VMD analysis jobs involving analysis of thousands
      of structures, e.g. loading and searching large subsets of the PDB.

  New representations and display features
    o Updated implementation of "GLSL" OpenGL programmable shading rendering
      mode now matches the standard rendering mode much more closely and
      has increased shading performance by up to 30%.
    o New "FieldLines" representation for display of potential field lines,
      and other volumetric gradient or flow information extracted from
      volumetric density maps.
    o Improved analysis and display of nucleic acid structures
    o Volume slice representations and coloring by volumetric data
      are now 20 to 30 times faster in most cases
    o New gradient background feature allows the background color to be drawn
      with a smoothly shaded vertical gradient. This can be useful
      in live presentations, where the VMD background gradient can be
      matched to PowerPoint slides being shown simultaneously on a second
      screen.
    o Newly developed scene export for the NVIDIA Gelato
      GPU-accelerated final frame rendering system.
    o New Tachyon scene file format and VMD scene export feature
      reduces scene file sizes to one tenth of of the size created
      by prior versions of VMD and Tachyon. This is particularly
      beneficial for renderings of large MSMS, Surf, Isosurface,
      NewRibbons, and NewCartoon representations.
    o Greatly improved RenderMan RIB format scene export capability
      matches on-screen lighting and display much more closely.
    o Trajectory playback performance up to 2x faster on some machines
      with very large structures and simple representations.

  New and improved analysis commands
    o New volmap 'coulomb' potential map calculation command calculates
      the electrostatic field for the supplied atom selection. The
      implementation is multithreaded, and also supports NVIDIA CUDA
      GPU acceleration in VMD binaries compiled with CUDA support.
    o New 'mol bondsrecalc' command allows forced recalculation of bonds
      based on the current timestep.
    o New 'measure energy' command, with bond, angle, dihed, imprp, vdw,
      and elect terms, based on the CHARMM force field. Allows energies
      to be computed over a range of trajectory frames.
    o New 'measure' commands for more efficient evaluation of bond lengths,
      angles, dihedrals, and impropers over a range of trajectory frames.
    o The "measure fit" RMS fitting command now runs up to two times faster
      than previous versions of VMD.
    o The "$sel move" atom selection subcommand for moving selections now
      runs up to two times faster than previous versions of VMD in the most
      common cases.
    o Added a new "-withradii" parameter to the "measure minmax" command
      to optionally calculate the bounding box that encloses the entire
      extents of the molecule, rather than just the atom centers.
    o Improved the performance of "measure minmax" by a factor of two.
    o Added -debye and -elementary dipole moment units flags to the
      "measure dipole" command for improved ease of use. Default mode
      remains -elementary for backwards compatibility.

  Other features and improvements
    o Added new commands implementing a built-in VMD
      collaboration/remote-control mechanism similar to the "vmdcollab"
      Tcl scripts, but in the low-level event loop
    o New VMDFORCECPUCOUNT environment variable allows users to override
      the default behavior of VMD to force it to use a subset or superset
      of the available number of processors to aid in multiprocessor
      performance tuning and testing.
    o Added event filtering logic to the Spaceball interface to prevent
      VMD from acting on null motion event packets on Win32.
    o Added new routines to query the number of megabytes of unused system
      memory, and total system memory. On systems that support the syscalls
      that query the stats, these functions can be used to warn the user if
      they are about to load a trajectory that's far too large to fit into
      the remaining physical memory.

  New and improved plugins and extensions
    o New "dowser" plugin adds solvent for DNA and RNA structures
      using the external program Dowser, by Jan Hermans of UNC.
    o BioCoRE chat plugin: misc user interface improvements
    o cgtools: new graphical user interface for coarse graining plugin.
      The new version supports both shape based and residue based methods,
      and can work with Cryo-EM density maps as input.
    o molefacture: numerous bug fixes, scalability, and performance
      improvements
    o multiplot: automatic color cycling, improved predefined colors,
      allow drawing of arbitrary items into the multiplot Tk canvas.
      Add multiplot legends to exported xmgrace plot files.
      (Jerome Henin's patch)
    o paratool: many small bug fixes and improvements
    o psfgen: Extend PSF_RECORD_LENGTH to not cut off long file
      names in remarks.
    o qmtool: many small bug fixes and improvements
    o solvate: will automatically switch to a hexadecimal segname generation
      scheme when too many segments would be created for the max segname
      string length. Solvate now calls resetpsf to free memory prior to
      loading the newly created water box, in order to save memory.
    o timeline: applied Charles McCallum's patch to improve the match
      between timeline secondary structure coloring and the VMD structure
      representation change color of 3_10 helices to blue as suggested
      by Charles Mccallum (and synced with new timeline plugin coloring)
    o VDNA plugin: Now supports options to include random variations in
      1) the linker length and/or 2) the wrapping of DNA around the
      histone core. This enables users to investigate the two-angle model
      of chromatin as described as early as Woodcock PNAS 1993,
      or Leuba PNAS 1994 or Helmut Schiessels work.

  New and improved file import and export
    o BRIX plugin now recognizes ".brx" extensions as well.
    o New CHARMM PBEQ potential map reader plugin
    o Updated CHARMM 31 expanded format PSF reading code to correctly read the
      atom type field.
    o Updated GAMESS plugin supports the new GAMESS_US version output
      7-SEP-2006-(R4) properly.
    o Added support for reading and writing binary DX files.
      (Justin Gullingsrud's patch)
    o Improve the behavior of atom assignment
      in the LAMMPS dump reader plugin. (Lutz Maibaum's patch)
    o mol2plugin: Remove autotyping. When this plugin was initially written
      VMD didn't have anything resembling true autotyping, Now that the
      IDATM exists, the right way to do things is just write VMD's types.
    o Prevent long segment names from overflowing the PDB segname field.
      (Axel Kohlmeyer's patch)
    o Add CRYST1 parsing to the PQR plugin. (Axel Kohlmeyer's patch)
    o Added support for reading binary UHBD grids. (Justin Gullingsrud's patch)
    o VASP potcar/poscar/chgcar plugins improvements to add
      "spin up" and "spin down" volume sets. Fix reading potcar files.
      (Rob Lahaye's patch)
    o XYZ plugin now exports atomic element data when available
      (Axel Kohlmeyer's patch)

  Bug Fixes
    o Fixed processing of callbacks when "mol delete all" was called,
      invoking an optimized routine to delete molecules which helps
      significantly when thousands of molecules are loaded.
    o Fixed a memory leak in the "sidechain" atom selection keyword
    o Fixed missing test for exclusion of H-H bonds in automatic bond
      determination code.
    o Fixed occasional incorrect material property specification in
      RenderMan RIB files exported by VMD
    o Fixed a potential crash caused by a bug in the command string tokenizer
      used by AtomColor and AtomRep
    o Force color regen when atomic number is updated
    o Force color regen and rep updates when an atom selection updates
      the atomic element name field.
    o MolFilePlugin now aborts loading a structure if namelist indices
      overflow or other data structure inconsistencies arise,
      to prevent bad data from being used.

Known bugs
----------
  Visit the VMD page for information on known bugs, workarounds, and fixes:
    http://www.ks.uiuc.edu/Research/vmd/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078